Souter was there, everyone but Kennedy was there.
I watched the whole thing and did not see him. They were on the stairs in order: Brewer, Ginsburg, Thomas, Scalia, O'Connor and Stevens. Were did you see Souter?
When I was watching on C-Span and they were bringing up the coffin to lay in state and I could be wrong about this, but the Justices there and they were lined up on the steps from the latest appointed to the earliest, was this Breyer, Ginsberg, Thomas, Scalia, O'Connor, and Stevens.
http://us.cnn.com/2005/POLITICS/09/06/rehnquist.funeral.ap/index.html
"Lining the steps were six justices of the Supreme Court...Absent were Justices Anthony M. Kennedy and David Souter.